The current evolutionary theories have remained incomplete, controversial, and stagnant for multiple decades. To solve this issue, we create the concept of carbon-based entities (CBEs) which include methane, amino acids, proteins, organisms, and other entities containing carbon atoms. We deduce from thermodynamics the driving force, the progressive mechanisms, and the major steps of evolution of CBEs, and hence establish a comprehensive evolutionary theory termed the CBE evolutionary theory (CBEET). The CBEET demonstrates that evolution is driven hierarchy-wise by thermodynamics and favors fitness and diversity. It provides novel explanations for origin of life (abiogenesis), macroevolution, natural selection, sympatric speciation, evolution tempos, animal group evolution, and human society development in a comprehensive and comprehensible way. It elucidates that collaboration, altruism, obeying rules with properly increased freedom are important throughout evolution of CBEs. It refutes thoroughly the wrong notion that negative entropy (negentropy) leads to biological order which is distinct from thermodynamic order. It integrates with research advances in multiple disciplines and bridges laws of physics, evolution in biology, and harmonious development of human society.